Green light for improving our understanding of AMR spread
Authors: Gabriela B Kraychete, Raquel R Bonelli, Renata C Picão
Journal: The Lancet Microbe (2023)

The discovery and use of antibiotics brought about a groundbreaking transformation in the treatment of bacterial infections, substantially reducing the number of deaths associated with microorganism-related diseases in humans and animals. However, the emergence and spread of antimicrobial resistance (AMR) impacts the effectiveness of these drugs and threatens many achievements of modern medicine, justifying the urgent need to prevent its spread.1Antimicrobial Resistance CollaboratorsGlobal burden of bacterial antimicrobial resistance in 2019: a systematic analysis.Lancet. 2022; 399: 629-655Summary Full Text Full Text PDF PubMed Scopus (3266) Google Scholar, 2O'Neill J Antimicrobial resistance: tackling a crisis for the health and wealth of nations.https://amr-review.org/sites/default/files/AMR%20Review%20Paper%20-%20Tackling%20a%20crisis%20for%20the%20health%20and%20wealth%20of%20nations_1.pdfDate: December, 2014Date accessed: October 16, 2023Google Scholar The consistent detection of clinically relevant antimicrobial resistance genes and their bacterial hosts in humans, animals, and the environment suggests that One Health approaches are essential for tackling AMR.3Larsson DGJ Gaze WH Laxminarayan R et al.AMR, One Health and the environment.Nat Microbiol. 2023; 8: 754-755Crossref PubMed Scopus (3) Google Scholar However, as AMR is also a naturally occurring process, an important question arises: what are the risks and consequences of AMR spread across different One Health sectors? Understanding the fundamental mechanisms of AMR spread is essential for developing effective methods to prevent it. Qiu E Yang and colleagues4Yang QE Ma X Zeng L et al.Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent transmission study.Lancet Microbe. 2023; (published online Nov 22.)https://doi.org/10.1016/S2666-5247(23)00227-6Google Scholar have made an important contribution to this knowledge gap. They addressed the horizontal dissemination of an IncX3 plasmid carrying the clinically relevant carbapenemase-encoding gene blaNDM-5. The plasmid was labelled with the green fluorescent protein (GFP)-encoding gene using a CRISPR-based editing system, receptors were counted and captured using fluorescence-activated cell sorting, and the new hosts of the plasmid were identified by 16S rRNA gene amplicon sequencing. Using this culture-independent approach in a simulated hospital sewage environment, Yang and colleagues4Yang QE Ma X Zeng L et al.Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent transmission study.Lancet Microbe. 2023; (published online Nov 22.)https://doi.org/10.1016/S2666-5247(23)00227-6Google Scholar described the transfer of a replicon previously classified as having a narrow host range to 16 phyla, including Gram-positive and poorly cultivable bacteria. Under stress conditions exerted by sodium hypochlorite, which was used to simulate the environment of wastewater treatment plants, the relative abundance of Gram-positive bacteria carrying the plasmid was higher than under non-stressed conditions. Notably, an Enterococcus faecalis strain that received the blaNDM-5-carrying IncX3 plasmid was able to transfer it back to Escherichia coli. These findings question the traditional view of horizontal AMR spread, in which DNA exchange between Gram-negative and Gram-positive bacteria is thought to occur only rarely, and suggest that the use of sodium hypochlorite to treat wastewater could favour trans-Gram plasmid transfer. Therefore, both the results obtained and the methods applied have transcended the original scope of the research question posed by the authors, inspiring and providing insights for further studies that will change the way we understand the dissemination of AMR genes in complex environments. From a practical perspective, CRISPR-based genome editing5Vo PLH Ronda C Klompe SE et al.CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering.Nat Biotechnol. 2021; 39: 480-489Crossref PubMed Scopus (131) Google Scholar opens the door to an array of possibilities for studying mobile genetic elements, particularly when combined with the dual-labelling, cultivation-independent conjugation method.6Sørensen SJ Bailey M Hansen LH Kroer N Wuertz S Studying plasmid horizontal transfer in situ: a critical review.Nat Rev Microbiol. 2005; 3: 700-710Crossref PubMed Scopus (533) Google Scholar, 7Klümper U Dechesne A Riber L et al.Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner.ISME J. 2017; 11: 152-165Crossref PubMed Scopus (0) Google Scholar The flexibility of the CRISPR-based editing approach enables the tracking not only of plasmids but also of any mobile genetic element provided its nucleotide sequence is available. This approach also could allow us to analyse AMR spread across different microbial communities and assess the contribution of other structures thought to influence it, given the design of appropriate CRISPR spacers. The insights presented by Yang and colleagues4Yang QE Ma X Zeng L et al.Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent transmission study.Lancet Microbe. 2023; (published online Nov 22.)https://doi.org/10.1016/S2666-5247(23)00227-6Google Scholar raise many additional questions. What can we expect regarding the transferability of other plasmid groups? How will such plasmids behave in microbiomes derived from other sources? How does this trans-Gram transfer affect plasmid evolution? In this regard, what is the role of systems that promote the maintenance and stability of plasmids? How stable are AMR plasmids in unexpected hosts and uncultivable bacteria, and what are the costs to these hosts? Do these hosts adapt to keep such replicons? What are the true reservoirs and vectors of AMR genes in complex microbial communities? Could other mobile genetic elements—such as transposons, transducing viruses, and extracellular vesicles—contribute to AMR spread? Future research efforts should focus on several key areas. Establishing the host range of replicons classified under various plasmid taxonomic units8Garcillán-Barcia MP Redondo-Salvo S de la Cruz F Plasmid classifications.Plasmid. 2023; 126102684Crossref PubMed Scopus (1) Google Scholar and investigating the role of different mobile genetic elements in the spread of these replicons will be important. Tracking the spread of plasmids and other mobile genetic elements in various environments—such as the sites of human and animal bodies, different types of waste, bodies of water, and soil under various anthropogenic pressures—will also be crucial, especially in response to interventions aimed at addressing AMR. Efforts should be directed towards developing strategies that accurately simulate the complex microbial communities that drive AMR in real-world situations under the One Health perspective. Detailed examination of AMR in this context is essential to effectively address the challenge posed to humanity by antimicrobial resistance. We declare no competing interests. Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission studyOur culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors. Full-Text PDF Open Access